ó gbc@sddlmZmZddlZddlZejdejƒZejdejƒZd„Z ejdejƒZ ejdejƒZ d„Z ejd ƒZ ejd ejƒZejd ƒZejd ejejƒZd „Zdeefd„ƒYZd„Zed„ZdS(iÿÿÿÿ(tLocationtlocationGeneratorNs#^(FT| ) [^ ].+ ((FT| ) .+ )+s^FTccsAx:tj|ƒD])}|jƒ}tjd|ƒ}|VqWdS(sÀ Iterate through a textual description of a feature table in a genbank or embl format. Return at each step a text representation of each individual feature composing the table. @param fttable: a string corresponding to the feature table of a genbank or an embl entry @type fttable: C{str} @return: an iterator on str @rtype: iterator @see: L{ftParser} s N(t_featureMatchertfinditertgroupt_featureCleanertsub(tfttabletmtt((s8lib/python2.7/site-packages/obitools/location/feature.pyttextFeatureIterator s s(?<=^ {21}/).+( {21}[^/].+)*s^ +ccsáxÚtj|ƒD]É}|jƒ}tjd|ƒ}|jddƒ}t|ƒdkrk|ddf}ni|ddkr”|djddƒ}n|djddƒ}yt |ƒ}WnnX|d|f}|VqWdS( s€ Parse a textual description of a feature in embl or genbank format as returned by the textFeatureIterator iterator and iterate through the key, value qualified defining this location. @param qualifiers: substring containing qualifiers @type qualifiers: str @return: an iterator on tuple (key,value), where keys are C{str} @rtype: iterator tt=iit translations t N( t_qualifierMatcherRRt_qualifierCleannerRtsplittlentNonetreplaceteval(t qualifiersRR tvalue((s8lib/python2.7/site-packages/obitools/location/feature.pytqualifierIterator$s  s (?<=^ {5})\S+s(?<=^.{21})[^/]+s[\s ]+s^ +/.+cCsŠtj|ƒjƒ}tj|ƒjƒ}tjd|ƒ}tj|ƒ}|dk rf|jƒ}nd}tj d|ƒ|||fS(NR s3Qualifiers regex not matching on ===== %s ========( t _ftmatchertsearchRt _locmatchert _cleanlocRt_qualifiersMatcherRtloggingtdebug(tfeaturetfttypetlocationR((s8lib/python2.7/site-packages/obitools/location/feature.pytftParserHs tFeaturecBsÚeZd„Zd„Zed„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z d „Z d „Zd „Zeeddd ƒZd„Zd„Zd„ZeedddƒZeedddƒZRS(cCs||_||_dS(N(t_fttypet_loc(tselfttypeR"((s8lib/python2.7/site-packages/obitools/location/feature.pyt__init__Ws cCs|jS(N(R%(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyt getFttype[scCs2|jj|ƒ}|r.|jƒj|ƒn|S(N(R&textractSequencetgetInfotupdate(R'tsequencet withQualifiertseq((s8lib/python2.7/site-packages/obitools/location/feature.pyR+_scCs |jjƒS(N(R&tisDirect(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR1escCs |jjƒS(N(R&tisSimple(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR2hscCs |jjƒS(N(R&t isFullLength(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR3kscCs,t|j|jjƒƒ}|j|ƒ|S(N(R$R%R&tsimplifyR-(R'tf((s8lib/python2.7/site-packages/obitools/location/feature.pyR4ns cCs t|jƒS(N(tstrR&(R'((s8lib/python2.7/site-packages/obitools/location/feature.pytlocStrsscCs |jjƒS(N(R&t needNucleic(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR8vscCs t|ƒS(N(trepr(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyt__str__yscCs(t|jt|jƒtj|ƒfƒS(N(R6tftTypeR&tdictt__repr__(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR=|scCs|jj|ƒS(N(R&t__cmp__(R'ty((s8lib/python2.7/site-packages/obitools/location/feature.pyR>scCs |jjƒS(N(R&t _getglocpos(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyR@‚ssFeature type namecCse|jƒ|dks&td|ƒ‚|dkr6|St|j|jj|ƒƒ}|j|ƒ|S(Nisshift to large (%d)(tgetBegintAssertionErrorR$R%R&tshiftR-(R'tsR5((s8lib/python2.7/site-packages/obitools/location/feature.pyRC‡s &  cCs |jjƒS(N(R&RA(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyRAscCs |jjƒS(N(R&tgetEnd(R'((s8lib/python2.7/site-packages/obitools/location/feature.pyRE“ss"beginning position of the locationsending position of the locationN(t__name__t __module__R)R*tFalseR+R1R2R3R4R7R8R:R=R>R@tpropertyRR;RCRAREtbegintend(((s8lib/python2.7/site-packages/obitools/location/feature.pyR$Vs&               cCsst|ƒ\}}}t|ƒ}t||ƒ}||_x3t|ƒD]%\}}|j|gƒj|ƒqFW|S(N(R#RR$trawRt setdefaulttappend(tfeatureDescriptionR!R"RR tktv((s8lib/python2.7/site-packages/obitools/location/feature.pytfeatureFactoryšs  ccsvxot|ƒD]a}yt|ƒ}WnCtk rh}tjd|ƒ|sU|‚ntjdƒq nX|Vq WdS(Ns=Parsing error on feature : =============== %s ===============s ===> Error skipped(R RRRBRR(t featureTablet skipErrorttftR te((s8lib/python2.7/site-packages/obitools/location/feature.pytfeatureIterator¥s  (tobitools.locationRRRtretcompiletMRRR RRRRtDOTALLRRRR#R<R$RRRHRW(((s8lib/python2.7/site-packages/obitools/location/feature.pyts      D